The CD8+ T lymphocyte subset can play an important role in immunosurveillance against tumorigenesis and virus infection (Pardoll, D. Annu. Rev. Immunol. 21, 807-839 (2003); Wong, P. & Pamer, E. Annu. Rev. Immunol. 21, 29-70 (2003)). Peptides presented by major histocompatibility complex (MHC) class I molecules on diseased cells can be recognized by CD8+ T cells (Yewdell, J. W. & Haeryfar, S. M. Annu. Rev. Immunol. 23, 651-682. (2005)). Selectivity of CTL for antigen-expressing cells can be directed toward targeted mortality in anti-virus or cancer therapy, if antigens are known.
A key step in developing T cell therapies is therefore to identify CTL-recognized antigens selectively expressed by a desired target cell, such as a tumor cell or virus infected cell. Typically, identification of such antigens has involved screening cDNA libraries as cDNA pools through a lengthy multi-step process in multi-well plates (Van den Eynde, B. Lethe, B., Van Pel, A., De Plaen, E. & Boon, T. J. Exp. Med. 173, 1373-1384 (1991); Boon, T. & van der Bruggen, P. J. Exp. Med. 183, 725-729 (1996); Van der Bruggen, P. et al. Immunol. Rev. 188, 51-64 (2002). Antigen-specific CTLs detect the presence of antigen-encoding DNA sequences in each cDNA pool. Hundreds of genes in individual cDNA pools compete for expression in antigen presenting cells (APC), causing difficulty in identifying rarely expressed antigens. In addition, low throughput in assessment of CTL cytotoxicity using current methods hampers antigen identification.
Although microarrays have been used successfully to examine gene expression profiles on a genome-wide scale, exploitation of microarrays for cell-based functional screens is yet to be fully realized. Previously, T cell responses to recombinant MHC molecules bound with defined peptide antigens spotted on microarrays have been demonstrated (Soen et al. PLoS Biology 1, E65 (2003); Stone et al. Proc. Natl. Acad. Sci. USA 102, 3744-3749 (2005)). Such approaches are useful in detecting the presence of T cells that recognize a known antigen. Although random peptide libraries could be screened in an MHC protein array as an approach to identify novel T cell antigens, such a screen would not be able to detect antigens generated by natural processing events in live APC and identify their encoding cDNAs.
There is a need in the field for methods for sensitive and rapid identification of CTL antigens. The present invention addresses this need.